MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b3752 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2937 b3908 b1656 b1982 b4139 b1033 b1623 b4014 b0261 b2976 b2799 b3945 b1602 b4381 b2406 b3915 b0452 b0509 b3125 b0529 b2492 b0904 b2954 b1380 b2660 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.417305 (mmol/gDw/h)
  Minimum Production Rate : 0.156069 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.028863
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.069875
  EX_pi_e : 0.402534
  EX_so4_e : 0.105086
  EX_k_e : 0.081455
  EX_fe3_e : 0.006702
  EX_mg2_e : 0.003620
  EX_ca2_e : 0.002172
  EX_cl_e : 0.002172
  EX_cu2_e : 0.000296
  EX_mn2_e : 0.000288
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.842894
  EX_co2_e : 36.607864
  EX_h_e : 5.803101
  EX_ade_e : 0.312604
  DM_5drib_c : 0.312417
  DM_4crsol_c : 0.312230
  EX_ac_e : 0.242949
  Auxiliary production reaction : 0.156069

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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